Although the layer‐by‐layer (LBL) processing can usually achieve an optimal bulk‐heterojunction morphology for high‐performance Organic photovoltaics (OPVs), the unambiguous working principles governing the morphology evolution are still lacking. To address this issue, here the phase‐separation kinetics of LBL processing are comprehensively studied using in situ spectroscopies, which are very sensitive to the intermolecular interactions, e.g. the molecular packing and D:A phase‐separation. Upon casting the nonfullerene acceptor (i.e., the BTP‐eC9) solution on top of the polymer donor, i.e., PM6, it is found that 1) the solvent will first swell the polymer and induce a polymer gel, 2) following the polymer gelation, the NFAs will immediately permeate into the cavities of polymer gel and form a molecular‐level D:A mixing, and 3) with the evaporation of the solvent, phase‐separation between the donor and acceptor occurs and results in a bulk‐heterojunction morphology as those achieved with blend‐cast processing. With these understandings, more diverse processing conditions have been purposely utilized to dictate the phase evolution process precisely. As a result, a high efficiency of 19.7% is reached, representing one of the best among binary OPVs. Therefore, this work deciphers phase‐separation kinetics of LBL processing and should pave the way toward advanced morphology control for high‐performance OPVs.